Another brake upgrade question

I am looking for a little help. I just finished a 5 lug upgrade using 99 front calipers and 95 rear calipers on my 93 Fox. I used a 1993 Cobra MC and brake booster. I bench bleed the mc and bleed the calipers numerous times and here is the question. With the car off and pushing on the brake, it is nice and solid, right at the top. The pedal holds pressure, not going to the floor. Once the car is started, the pedal loses pressure to about half way. Stopping power is poor at best. Where should I look next? I looked at the brake booster pushrod for adjustment, just not sure how to adjust. When I put the mc on the booster, it feels like there is pressure on it when I tighten the two bolts down, almost like to rod is pushing again the mc. Would this create the problem I am having?
Sorry this is so long, I just want to be specific so there is no confusion.
I also have a wildwood prop valve adjusted all the way in, if that matters.
Thanks in advance.
 
I used mjbobbitt's 3-2 conversion piece and I gutted the prop valve as directed with a Ford racing parts plug and removal of spring and shaft.
I also have MM stainless steel brakes lines in front and all new lines in the rear.
Anybody with any suggestions?
How do you adjust the pushrod of the bralke booster? Just by turning it? Any help or suggestions would be great. Thanks
 
There is an adjustment proceedure for the Booster rod on Maximum Motorsports web page, and you need to adjust your Prop Valve per M-2300-K Instructions on Ford Racing Website.